I've used Apple's Backup 2 to backup some personal files (adresses, calendars, safari bookmarks..) on my Disk... it would be very fine if Backup was not stupid enough top backup cache file !!!
1) REMOVE Safari Settings from your list all together.
2) Drag & Drop the REAL safari setting files that you ACTUALLY want to keep backing up such as favorites, bookmarks, etc. You can drag these into the backup window as new things to backup with their own check boxes. The official safari settings feature is just for convenience ... its not the ONLY way to do it.